6D5M

Ras:SOS:Ras in complex with a small molecule activator


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery and Structure-Based Optimization of Benzimidazole-Derived Activators of SOS1-Mediated Nucleotide Exchange on RAS.

Hodges, T.R.Abbott, J.R.Little, A.J.Sarkar, D.Salovich, J.M.Howes, J.E.Akan, D.T.Sai, J.Arnold, A.L.Browning, C.Burns, M.C.Sobolik, T.Sun, Q.Beesetty, Y.Coker, J.A.Scharn, D.Stadtmueller, H.Rossanese, O.W.Phan, J.Waterson, A.G.McConnell, D.B.Fesik, S.W.

(2018) J Med Chem 61: 8875-8894

  • DOI: 10.1021/acs.jmedchem.8b01108
  • Primary Citation of Related Structures:  
    6D55, 6D56, 6D59, 6D5E, 6D5G, 6D5H, 6D5J, 6D5L, 6D5M, 6D5V, 6D5W

  • PubMed Abstract: 
  • Son of sevenless homologue 1 (SOS1) is a guanine nucleotide exchange factor that catalyzes the exchange of GDP for GTP on RAS. In its active form, GTP-bound RAS is responsible for numerous critical cellular processes. Aberrant RAS activity is involved in ∼30% of all human cancers; hence, SOS1 is an attractive therapeutic target for its role in modulating RAS activation ...

    Son of sevenless homologue 1 (SOS1) is a guanine nucleotide exchange factor that catalyzes the exchange of GDP for GTP on RAS. In its active form, GTP-bound RAS is responsible for numerous critical cellular processes. Aberrant RAS activity is involved in ∼30% of all human cancers; hence, SOS1 is an attractive therapeutic target for its role in modulating RAS activation. Here, we describe a new series of benzimidazole-derived SOS1 agonists. Using structure-guided design, we discovered small molecules that increase nucleotide exchange on RAS in vitro at submicromolar concentrations, bind to SOS1 with low double-digit nanomolar affinity, rapidly enhance cellular RAS-GTP levels, and invoke biphasic signaling changes in phosphorylation of ERK 1/2. These compounds represent the most potent series of SOS1 agonists reported to date.


    Related Citations: 
    • Approach for targeting Ras with small molecules that activate SOS-mediated nucleotide exchange.
      Burns, M.C., Sun, Q., Daniels, R.N., Camper, D., Kennedy, J.P., Phan, J., Olejniczak, E.T., Lee, T., Waterson, A.G., Rossanese, O.W., Fesik, S.W.
      (2014) Proc Natl Acad Sci U S A 111: 3401

    Organizational Affiliation

    Department of Chemistry , Vanderbilt University , Nashville , Tennessee 37232-0146 , United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GTPase HRasA [auth Q]167Homo sapiensMutation(s): 0 
Gene Names: HRASHRAS1
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01112 (Homo sapiens)
Explore P01112 
Go to UniProtKB:  P01112
PHAROS:  P01112
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
GTPase HRasB [auth R]167Homo sapiensMutation(s): 0 
Gene Names: HRASHRAS1
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01112 (Homo sapiens)
Explore P01112 
Go to UniProtKB:  P01112
PHAROS:  P01112
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Son of sevenless homolog 1C [auth S]482Homo sapiensMutation(s): 0 
Gene Names: SOS1
UniProt & NIH Common Fund Data Resources
Find proteins for Q07889 (Homo sapiens)
Explore Q07889 
Go to UniProtKB:  Q07889
PHAROS:  Q07889
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP (Subject of Investigation/LOI)
Query on GNP

Download Ideal Coordinates CCD File 
E [auth Q]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
FW4 (Subject of Investigation/LOI)
Query on FW4

Download Ideal Coordinates CCD File 
F [auth S]1-[(3-chloro-4-fluorophenyl)methyl]-5,6-dimethyl-2-(piperazin-1-yl)-1H-benzimidazole
C20 H22 Cl F N4
BQDQIRCHYJZDPW-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth Q]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
FW4 BindingDB:  6D5M EC50: min: 2200, max: 2.91e+4 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 183.134α = 90
b = 183.134β = 90
c = 178.329γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
United StatesLustgarten

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2018-11-07
    Changes: Data collection, Database references